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		<title>PDB2PQR</title>
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			<h1>PDB2PQR</h1>
			<h3>An automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations.</h3>
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		<HR>

		<p> PDB2PQR is a Python software package that automates many of the
		common tasks of preparing structures for continuum electrostatics
		calculations, providing a platform-independent utility for converting
		protein files in <a href="http://www.rcsb.org/pdb/">PDB format</a> to
		PQR format.  These tasks include:
		<ul>
			<li> Adding a limited number of missing heavy atoms to
			biomolecular structures
			<li> Determining side-chain pKas 
			<li> Placing missing hydrogens
			<li> Optimizing the protein for favorable hydrogen bonding
			<li> Assigning charge and radius parameters from a variety of
			force fields 
		</ul>

		<p> PDB2PQR was ported to Python by Todd Dolinsky while working with <a
			href="http://agave.wustl.edu">Nathan Baker</a> at Washington
		University in St. Louis.  The PDB2PQR code is based on C++ design and
		algorithms by <a href="http://enzyme.ucd.ie/">Jens Erik Nielsen</a>.
		PDB2PQR was originally designed to facilitate structure preparation for
		<a href="http://apbs.wustl.edu">APBS</a>.

		<p> PDB2PQR uses <a href="http://propka.ki.ku.dk">PROPKA</a> to
		determine protein pKa values.  PROPKA is developed by the <a
			href="http://propka.ki.ku.dk/~jhjensen/">Jensen Research
			Group</a> at the University of Copenhagen.  More information
		about PROPKA can be found at <a
			href="http://propka.ki.ku.dk/">http://propka.ki.ku.dk/</a>.<P>

		<p> PEOE_PB charges for 
		<!--biomolecue and -->
		ligand parameterization were
		developed by Paul Czodrowski in the <a
			href="http://www.agklebe.de">Klebe Group</a> at the Philipps University Marburg.


		<p> Please visit the following links for more information about PDB2PQR:
		<ul>
			<li>Documentation:
			<ul>
				<li> <a href="userguide.html">User
					Guide</a> </li>
				<li> <a href="programmerguide.html">Programmer
					Guide</a> </li>
				<li> <a href="examples/">Examples</a> </li>
			</ul>
			<li><a href="#availability">Availability</a>
			<li><a href="#mailing">Mailing lists</a>
			<li><a href="#citing">Further Reading/Citing PDB2PQR</a>
			<li><a href="#support">Supporting organizations</a>
			<li><a href="license.txt">License</a>
			<li> <a href="http://agave.wustl.edu/pdb2pqr-stats/usage/">PDB2PQR
				Usage Statistics</a> (WUSTL Mirror) </li>
		</ul>
		<hr>

		<a name="availability"></a>
		<h3>Availability</h3>

		<P> PDB2PQR is available as both a web service and as command-line
		software for download.  The PDB2PQR web server can be found at two
		mirrors:
		<ul> 
			<li> <a href="http://agave.wustl.edu/pdb2pqr/index.html">Washington
				University in St. Louis</a> (currently running
			version 1.7)
			<li><a href="http://nbcr.net/pdb2pqr">NBCR (UCSD)</a>
			(currently running
			version 1.7)
		</ul>

		<P>  The command line PDB2PQR tool is freely available for <a
			href="http://agave.wustl.edu/pdb2pqr-stats/register.html">download</a>. 

		<hr/>

		<a name="mailing"></a>
		<h3>Mailing Lists</h3>

		<P> There are two mailing lists associated with the PDB2PQR
		software:
		<ul>
			<li>pdb2pqr-announce, a low-traffic list for announcements
			regarding bugs and new versions of the software:  <a
				href="http://lists.sourceforge.net/lists/listinfo/pdb2pqr-announce">List
				web page</a>, <a
				href="http://sourceforge.net/mailarchive/forum.php?forum=pdb2pqr-announce">List
				archives</a> 
			<li>pdb2pqr-users, a list for discussion of PDB2PQR,
			troubleshooting, and reporting potential bugs:   <a
				href="http://lists.sourceforge.net/lists/listinfo/pdb2pqr-users">List
				web page</a>, <a
				href="http://sourceforge.net/mailarchive/forum.php?forum=pdb2pqr-users">List
				archives</a>
		</ul>

		<HR/>

		<a name="citing"></a> <h3>Further Reading/Citing PDB2PQR</h3><P>

		<p>Please acknowledge your use of PDB2PQR by citing:
			<ul>
				<li> <a href="http://dx.doi.org/10.1093/nar/gkm276">Dolinsky TJ, Czodrowski P, Li H, Nielsen JE, Jensen JH, Klebe G, Baker NA. PDB2PQR: Expanding and upgrading automated preparation of biomolecular structures for molecular simulations. <i>Nucleic Acids Res</i>,  <b>35</b>,  W522-5, 2007.</a> </li>
			<li> <a href="http://nar.oupjournals.org/cgi/content/abstract/32/suppl_2/W665">Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. PDB2PQR: an automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations. <i>Nucleic Acids Res</i>, <b>32</b>, W665-W667 (2004).</a> </li>
			</ul>
			</p>

		<p>Please acknowledge your use of PropKa by citing:
		<blockquote>
			<a href="http://dx.doi.org/10.1002/prot.20660">Li H, Robertson
				AD, Jensen JH. Very Fast Empirical Prediction and
				Rationalization of Protein pKa Values. <i>Proteins</i>,
				<b>61</b>, 704-721 (2005).</a>
		</blockquote>

		<p>Please acknowledge your use of PEOE_PB charges by citing:
		<blockquote>
			<a href="http://dx.doi.org/10.1002/prot.21110">Czodrowski P,
				Dramburg I, Sotriffer CA, Klebe G.  Development,
				validation, and application of adapted PEOE charges to
				estimate pKa values of functional groups in
				protein-ligand complexes. <i>Proteins</i>, <b>65</b>, 
				424-437 (2006).</a>
		</blockquote>
		<HR/>

		<a name="support"></a>
		<h3>Supporting Organizations</h3>

		<P> The development of PDB2PQR has been supported financially by:
		<ul>
			<li><a href="http://www.nih.gov/">National Institutes of
				Health</a> (grant GM069702-01)
			<li><a href="http://www.npaci.edu/">National Partnership for
				Advanced Computational Infrastructure</a> Alpha Project
			program
			<li><a href="http://nbcr.sdsc.edu/">National Biomedical
				Computation Resource</a>
		</ul>

		<hr/>

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